rs10878983

Variant names:

• chr12-69432313-G-A
• rs10878983

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.447 in 151,746 control chromosomes in the GnomAD database, including 15,408 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.45 (15408 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67792 AN: 151628 Hom.: 15388 Cov.: 30

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.457

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.447 AC: 67852 AN: 151746 Hom.: 15408 Cov.: 30 AF XY: 0.445 AC XY: 32996 AN XY: 74128

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.454

Alfa AF: 0.475 Hom.: 25200

Bravo AF: 0.447

Asia WGS AF: 0.417 AC: 1449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.41

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10878983; hg19: chr12-69826093;